Another longtime polygrapher said the National Reconnaissance Office had established an off-the-books policy that encouraged going after prohibited information.

“The organization says in writing that they’re not supposed to be asking about this information, when in fact behind closed doors they are pushing (polygraphers) to actively pursue it,” the polygrapher said.

Hinshaw, who said he’d witnessed the improper practices as a former acting supervisor, accused the agency of becoming so cavalier about following the rules that the polygraph branch chief, Michael McMahon, pressured him to change the results of the agency director’s polygraph if he failed the test. In the end, director Bruce Carlson passed, but Hinshaw said the incident demonstrated how the agency’s use of polygraph was arbitrary and wasn’t about protecting the country.

McMahon didn’t respond to emails and phone messages from McClatchy inquiring about the incident.

“There’s a line you have to draw,” said Hinshaw, who worked in the program from 2005 until earlier this year. “The original idea for using polygraph to clear people was to ferret out moles and spies. Now it’s morphing into an ambiguous exam where anything’s possible.”

The National Reconnaissance Office, meanwhile, has branded Phillips and Hinshaw troubled employees. Before Phillips resigned, the agency suspended him for three days, saying he was insubordinate, among other complaints, and it revoked Hinshaw’s security clearance earlier this year, citing his foreclosure on his family home.

Both men said they thought the agency had retaliated against them for trying to resist the polygraph practices, and records show that they’d voiced their concerns before the agency took action against them. The Pentagon’s inspector general is investigating Phillips’ complaint.

But even if the agency were found to be violating Pentagon policies, the laws that limit the government’s use of polygraph in screening aren’t specific on what constitutes an illegal abuse. The Privacy Act of 1974 requires that the government collect only personal information that’s necessary and relevant, and a 1981 presidential directive calls for “the least intrusive collection techniques feasible.”

Much of the interpretation of what that means has been left to the federal departments that run the polygraph programs.

“Some polygraph programs have been getting away with all sorts of abuses for years,” said Mark Zaid, an attorney for Phillips who’s been handling national security cases for 20 years. “It’s very difficult to hold them accountable.”

Why is the National Reconnaissance Office interested in such private details? In internal documents and emails, supervisors told polygraphers they felt pressure from the officials known as adjudicators, who make the final decisions on national security clearances.

The agency’s motives, however, are more complicated, some of the polygraphers said.

The Pentagon’s test is so restricted to counterintelligence issues that it’s notorious among polygraphers for compelling admissions of mundane and ultimately harmless infractions. One of the most common confessions involves harried bureaucrats who admit to taking classified documents home by mistake. By collecting confessions to repulsive or criminal behavior, officials can justify using polygraph screenings to their bosses, Congress and a skeptical public despite questions about the test’s reliability, the polygraphers said.